get_ana_rate

Internal function.
Calculates the anagenesis rate given the current number of
immigrant species and the per capita rate.

internal

Simulates and computes the (maximum) likelihood of a dynamical
model of island biota assembly through speciation, immigration and
extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.

Rampal Etienne

DAISIE

Dynamical Assembly of Islands by Speciation, Immigration and
Extinction

Rampal S. Etienne

Luis Valente

Albert B. Phillimore

Bart Haegeman

Joshua W. Lambert

Pedro Santos Neves

Shu Xie

Richèl J.C. Bilderbeek

Hanno Hildenbrandt

Torsten Hauffe

Giovanni Laudanno

Nadiah Kristensen

Ornela Dehayem Nanwou

Raphael Scherrer

get_ana_rate function

<dl><dt>laa</dt>
<dd>A numeric with the per capita anagenesis rate.</dd>
<dt>num_immigrants</dt>
<dd>A numeric with the current number of non-endemic
species (a.k.a non-endemic species).</dd>
<dt>island_spec</dt>
<dd>Matrix with current state of simulation containing number
of species.</dd>
<dt>trait_pars</dt>
<dd>A named list containing diversification rates considering
 two trait states created by <code>create_trait_pars</code>:<ul>
<li>[1]:A numeric with the per capita transition rate with state 1</li>
<li>[2]:A numeric with the per capita immigration rate with state 2</li>
<li>[3]:A numeric with the per capita extinction rate with state 2</li>
<li>[4]:A numeric with the per capita anagenesis rate with state 2</li>
<li>[5]:A numeric with the per capita cladogenesis rate with state 2</li>
<li>[6]:A numeric with the per capita transition rate with state 2</li>
<li>[7]:A numeric with the number of species with trait state 2 on
 mainland</li>
</ul></dd></dl>

Arguments

Pedro Neves, Joshua Lambert, Shu Xie

Author

Calculate anagenesis rate — get_ana_rate

<dl>

<dt>laa</dt>
<dd>A numeric with the per capita anagenesis rate.</dd>


<dt>num_immigrants</dt>
<dd>A numeric with the current number of non-endemic
species (a.k.a non-endemic species).</dd>


<dt>island_spec</dt>
<dd>Matrix with current state of simulation containing number
of species.</dd>


<dt>trait_pars</dt>
<dd>A named list containing diversification rates considering
 two trait states created by <code>create_trait_pars</code>:<ul>
<li>[1]:A numeric with the per capita transition rate with state 1</li>
<li>[2]:A numeric with the per capita immigration rate with state 2</li>
<li>[3]:A numeric with the per capita extinction rate with state 2</li>
<li>[4]:A numeric with the per capita anagenesis rate with state 2</li>
<li>[5]:A numeric with the per capita cladogenesis rate with state 2</li>
<li>[6]:A numeric with the per capita transition rate with state 2</li>
<li>[7]:A numeric with the number of species with trait state 2 on
 mainland</li>
</ul></dd>

</dl>

Calculate anagenesis rate

get_ana_rate: Calculate anagenesis rate

Description

Usage

Arguments

Author

See Also